There are other factors that contribute to cervical carcinogenesis except HPV infection. This study aimed to investigate the association between vaginal micro-environment factors, including H 2 O 2 , vaginal PH value, vagina cleanness, β-glucuronidase, coagulase, neuraminidase and leukocyte esterase and cervical intraeipithelial neoplasia (CIN). In total 1019 participants, including 623 normal cervical (NC) women, 303 patients with low-grade cervical intraepithelial neoplasia (CIN1) and 93 patients with high-grade cervical intraepithelial neoplasia (CIN2/3), were enrolled into the study. HPV genotyping was detected by flow-through hybridization and gene chip. Vaginal H 2 O 2 , β-glucuronidase, coagulase, neuraminidase and leukocyte esterase were detected by Aerobic Vaginitis (AV) / Bacterial Vaginal Disease (BV) Five Joint Test Kit. Vaginal PH was measured on the glass slide after microscopy, using color strips with a PH range of 3.8-5.4. Vagina cleanness was determined according to the National Clinical Laboratory Practice Guideline. χ 2 test and Logistic regression were operated using SPSS 22.0 software. Our results showed that HPV16 infection rate and the abnormal rates of H 2 O 2 , PH, vagina cleanness, β-glucuronidase or neuraminidase increased gradually along with the severity of CIN (P<0.05). Abnormities of H 2 O 2 , cleanness, β-glucuronidase and neuraminidase were risk factors for CIN regardless of HPV16 infection, furthermore, abnormities of PH value, leukocyte esterase could also increase the risk of CIN in HPV16 positive group. In addition, women with abnormal vaginal micro-environment factors in HPV16 positive group had a significantly higher risk of developing CIN than HPV16 negative group. The results from generalized multifactor dimensionality reduction (GMDR) model showed that there was interaction effect with abnormities of vagina cleanness, H 2 O 2 , β-glucuronidase and neuraminidase on CIN2/3 in HPV16 negative group, while, there was interaction effect with abnormities of vagina cleanness, β-glucuronidase and neuraminidase on CIN1 and with abnormities of vagina cleanness, PH, H 2 O 2 , β-glucuronidase, neuraminidase and leukocyte esterase on CIN2/3 in HPV16 positive group. Our results suggested that vaginal micro-environment disorder could increase the risk of CIN, especially, the abnormality of H 2 O 2 , cleanness, β-glucuronidase and neuraminidase. There were interaction effects with abnormities of H 2 O 2 , vagina cleanness, β-glucuronidase and neuraminidase on CIN whether HPV16 was infected or not.